For my flex application, I want that my client can save their
configuration files for the display and can use it next time. So
there must be a pop up window to show the file names and promte a
window for user to input the file name.

I know there are two possible ways to do this:
First, save the file to the web service and then download to
the local machine and reversely, upload the file to the web service
and then the flex application read those configuration files from
web service.

I don't know if this method will expose more information
about our server or not. Just I am not quite sure about the
security issue of this way.

Second, just simply save all the files to the web serive
according to the username, and then I use popUpManager to create
two popUp windows to interact with users in order to get the file
name.

It will cost space on the server if there are too many users.
Besides, I read a post in this forum pointed out that the
PopUpManager.removePopUp() method cannot free up memory as it
should be.

I am struggling with which method to use, or someone has a
better idea, please help me out here.

Besides, is there any way to make Flex builder debugging
faster?? It takes ages to debug even just several lines. It does
not have a good memory as well. If I take the breakpoint out this
time, it will appear in the next debugging time again!!

If I were implementing this I would send the data to the
server to save it and request it from the server the next time the
app started. This makes your app a much truer "web" application
because the user can return to their work from any computer. If you
download the file you won't be able to read it from the Flash
Player - you'll only have to upload it to the server and then
request it from the Player, so there's no real point to that.

In other words, you really have one choice: send to server to
save data, read from server to get it back. I'd think a server
would have gigabytes of space; how big can your data be?

Unless you expect someone to spend hours using your Flex app,
don't worry too much about memory. We know about this problem and
if hasn't been addressed by the current update on the web site,
then I'm sure it will fixed in the next one.